Pythonista has two different file storage options: "This iPad" and "iCloud".

Anything stored in the "iCloud" section appears in "iCloud Drive/Pythonista 3" in the Files app. However, for files stored in the "This iPad" section, there is no corresponding "On My iPad/Pythonista 3" folder.

This means that only scripts stored in iCloud Drive are accessible from the file picker, so apps like Working Copy can't work with local scripts. If Pythonista stored its local documents so that they correctly appeared in the Files app, Working Copy could see those local files as well.

That is an option, one that I intend to use at some point. I'm using it currently for Scriptable, and it works great. I can edit a Scriptable script on my iPhone, then I open up Working Copy on my iPad (where I set up the sync) and see the change ready to be committed.

One reason why (2) isn't a complete solution, is that Pythonista doesn't see iCloud in PYTHONPATH. In order to add user-defined modules, I believe they have to go in one of the site-packages directories in the device file system. But for version control of most scripts in Pythonista, the Working Copy sync function should work well with the Pythonista iCloud folder.